Loading doc/src/pair_python.txt +9 −9 Original line number Diff line number Diff line Loading @@ -80,7 +80,7 @@ class LAMMPSPairPotential(object): self.pmap=dict() self.units='lj' def map_coeff(self,name,ltype): self.pmap[ltype]=name self.pmap\[ltype\]=name def check_units(self,units): if (units != self.units): raise Exception("Conflicting units: %s vs. %s" % (self.units,units)) Loading @@ -91,7 +91,7 @@ from this class and should be initialize in a similar fashion to the example given below. NOTE: The class constructor has to set up a data structure containing the potential parameters supported by this class. It should also define a variable {self.units} containing a string matching one of the options of LAMMPS' "units command"_units.html, which matching one of the options of LAMMPS' "units"_units.html command, which is used to verify, that the potential definition in the python class and in the LAMMPS input match. Example for a single type Lennard-Jones potential class {LJCutMelt} in reducted units, which defines an atom Loading Loading @@ -121,19 +121,19 @@ value of the internal potential parameter data structure. Following the {LJCutMelt} example, here are the two functions: def compute_force(self,rsq,itype,jtype): coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\] r2inv = 1.0/rsq r6inv = r2inv*r2inv*r2inv lj1 = coeff[0] lj2 = coeff[1] lj1 = coeff\[0\] lj2 = coeff\[1\] return (r6inv * (lj1*r6inv - lj2))*r2inv :pre def compute_energy(self,rsq,itype,jtype): coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\] r2inv = 1.0/rsq r6inv = r2inv*r2inv*r2inv lj3 = coeff[2] lj4 = coeff[3] lj3 = coeff\[2\] lj4 = coeff\[3\] return (r6inv * (lj3*r6inv - lj4)) :pre IMPORTANT NOTE: for consistency with the C++ pair styles in LAMMPS, Loading @@ -149,7 +149,7 @@ IMPORTANT NOTE: The evaluation of scripted python code will slow down the computation pair-wise interactions quite significantly. However, this can be largely worked around through using the python pair style not for the actual simulation, but to generate tabulated potentials on the fly using the "pair_write command"_pair_write.html . Please on the fly using the "pair_write"_pair_write.html command. Please see below for an example LAMMPS input of how to build a table file: pair_style python 2.5 Loading Loading
doc/src/pair_python.txt +9 −9 Original line number Diff line number Diff line Loading @@ -80,7 +80,7 @@ class LAMMPSPairPotential(object): self.pmap=dict() self.units='lj' def map_coeff(self,name,ltype): self.pmap[ltype]=name self.pmap\[ltype\]=name def check_units(self,units): if (units != self.units): raise Exception("Conflicting units: %s vs. %s" % (self.units,units)) Loading @@ -91,7 +91,7 @@ from this class and should be initialize in a similar fashion to the example given below. NOTE: The class constructor has to set up a data structure containing the potential parameters supported by this class. It should also define a variable {self.units} containing a string matching one of the options of LAMMPS' "units command"_units.html, which matching one of the options of LAMMPS' "units"_units.html command, which is used to verify, that the potential definition in the python class and in the LAMMPS input match. Example for a single type Lennard-Jones potential class {LJCutMelt} in reducted units, which defines an atom Loading Loading @@ -121,19 +121,19 @@ value of the internal potential parameter data structure. Following the {LJCutMelt} example, here are the two functions: def compute_force(self,rsq,itype,jtype): coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\] r2inv = 1.0/rsq r6inv = r2inv*r2inv*r2inv lj1 = coeff[0] lj2 = coeff[1] lj1 = coeff\[0\] lj2 = coeff\[1\] return (r6inv * (lj1*r6inv - lj2))*r2inv :pre def compute_energy(self,rsq,itype,jtype): coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\] r2inv = 1.0/rsq r6inv = r2inv*r2inv*r2inv lj3 = coeff[2] lj4 = coeff[3] lj3 = coeff\[2\] lj4 = coeff\[3\] return (r6inv * (lj3*r6inv - lj4)) :pre IMPORTANT NOTE: for consistency with the C++ pair styles in LAMMPS, Loading @@ -149,7 +149,7 @@ IMPORTANT NOTE: The evaluation of scripted python code will slow down the computation pair-wise interactions quite significantly. However, this can be largely worked around through using the python pair style not for the actual simulation, but to generate tabulated potentials on the fly using the "pair_write command"_pair_write.html . Please on the fly using the "pair_write"_pair_write.html command. Please see below for an example LAMMPS input of how to build a table file: pair_style python 2.5 Loading
